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- PDB-1jv6: BACTERIORHODOPSIN D85S/F219L DOUBLE MUTANT AT 2.00 ANGSTROM RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1jv6
TitleBACTERIORHODOPSIN D85S/F219L DOUBLE MUTANT AT 2.00 ANGSTROM RESOLUTION
ComponentsBacteriorhodopsin
KeywordsION TRANSPORT / PHOTORECEPTOR / HALOARCHAEA / 7-TRANSMEMBRANE / F219L MUTANT / CUBIC LIPID PHASE
Function / homology
Function and homology information


light-driven active monoatomic ion transmembrane transporter activity / monoatomic ion channel activity / photoreceptor activity / phototransduction / proton transmembrane transport / plasma membrane
Similarity search - Function
Bacterial rhodopsins retinal binding site. / Bacterial rhodopsins signature 1. / Rhodopsin, retinal binding site / Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-LI1 / RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRouhani, S. / Cartailler, J.-P. / Facciotti, M.T. / Walian, P. / Needleman, R. / Lanyi, J.K. / Glaeser, R.M. / Luecke, H.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of the D85S mutant of bacteriorhodopsin: model of an O-like photocycle intermediate.
Authors: Rouhani, S. / Cartailler, J.P. / Facciotti, M.T. / Walian, P. / Needleman, R. / Lanyi, J.K. / Glaeser, R.M. / Luecke, H.
History
DepositionAug 28, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,26510
Polymers26,8671
Non-polymers5,3979
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.800, 121.300, 85.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Bacteriorhodopsin / BR


Mass: 26867.475 Da / Num. of mol.: 1 / Mutation: D85S,F219L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halobacterium salinarum (Halophile) / Gene: Bop / Plasmid: pNov-r / Production host: Halobacterium salinarum (Halophile) / References: UniProt: P02945
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical
ChemComp-LI1 / 1-[2,6,10.14-TETRAMETHYL-HEXADECAN-16-YL]-2-[2,10,14-TRIMETHYLHEXADECAN-16-YL]GLYCEROL / LIPID FRAGMENT


Mass: 639.130 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C42H86O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 293 K / Method: cubic lipid phase / pH: 5.6
Details: monoolein, octyl-beta-D-glucopyranoside, pH 5.6, cubic lipid phase, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Details: Landau, E.M., (1996) Proc.Natl.Acad.Sci.USA., 93, 14532.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.3 Msodium potassium Pi11
23.5 mg/mlprotein11
30.05 %methylpentandiol11
41.2 %beta-octylglycopyranoside11

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Apr 7, 1999
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 18717 / Num. obs: 14934 / % possible obs: 79.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.1 % / Rsym value: 0.077 / Net I/σ(I): 14.4
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 2.6 / Num. unique all: 769 / Rsym value: 0.558 / % possible all: 42
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 99 Å / Num. measured all: 152520 / Rmerge(I) obs: 0.077
Reflection shell
*PLUS
% possible obs: 70.8 % / Rmerge(I) obs: 0.558

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Processing

Software
NameVersionClassification
X-PLORmodel building
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JV7 (Bacteriorhodopsin D85S coordinates, without diether lipids nor water)

1jv7


Resolution: 2→12 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
Details: Intensities (I) and not amplitude (F) was used in refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.24 682 5 %random
Rwork0.222 ---
all0.25 18546 --
obs0.244 13778 --
Refinement stepCycle: LAST / Resolution: 2→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1613 0 141 34 1788
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.103
X-RAY DIFFRACTIONc_bond_d0.0065
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 12 Å / σ(F): 1 / % reflection Rfree: 5 % / Rfactor obs: 0.222 / Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS

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